"Malcolm, the front page of today's paper does not represent our community. We are delighted to have you here," she said.
"I just wanted to apologise for that paper. The sentiment that says we need help is real but that image was inexcusable so please accept our apology."
The Prime Minister reportedly thanked the mayor for her "very gracious" apology but said it was "not needed".
The Morning Bulletin today carried the headline "Stop Clowning Around Malcolm" and said it was time the prime minister got serious about giving Central Queensland a fair go.
Responding to the front page, The Australian newspaper said it "echoed The New Zealand Herald's notorious cartoon depicting Wallabies coach Michael Cheika as a clown, which received widespread media attention".
The paper said it also referenced the so-called 'creepy crown phenomenon' which has become a global sensation.
In its editorial, The Morning Bulletin said it did not think Turnbull was a clown.
"But Wallaby rugby coach Michael Cheika's reaction to a similar drawing in New Zealand last weekend ... put it on the front pages and TV screens of most Australians," the editorial said, referencing the Herald cartoon controversy.
"We hope this gimmick gets your attention today - desperate times call for unusual tactics."
The paper hoped the gimmick would draw attention to the plight of regional Australia, "particularly those communities smashed by the mining downturn in Central Queensland".
"The big question is: Are you going to do anything about it?" the editorial asked.
It said residents of regional Australia die earlier than those in Mr Turnbull's electorate of Wentworth in Sydney, were poorer, had worse health outcomes and less employment opportunities.
"There are any number of reasons Pauline Hanson's One Nation party is surging in the polls in this area," it said.
"A lack of faith our people have that the two main parties will make a difference is a key one of those.
"Regional Australians are desperate to find someone to give them a Fair Go. Are you the man for the job?"
In an interview yesterday Deputy Prime Minister Barnaby Joyce denied the PM's Queensland visit was about countering the rise of the One Nation vote.
A recent Newspoll showed the primary vote for Pauline Hanson's party had jumped to 10 per cent in Queensland, up from 5.5 per cent at the election.
Joyce said it was important and "healthy" for MPs to get out to regional areas.
"The prime minister will go very well ... talk to some of the cattle producers, talk to people in little regional towns," he told reporters in Canberra.
Today Turnbull announced a multi-million dollar fund for new dams and water projects across the country in Rockhampton.
The fund is designed to break ground on water infrastructure such as dams, water treatment, and managed aquifer recharge projects.
The government has already given in-principle backing to five water projects including the Rookwood Weir in Queensland, Dungowan Dam in NSW, the Macalister Irrigation District in Victoria, among others.
The Morning Bulletin is owned by Australian Regional Media. News Corp Australia, which publishes The Australian, has proposed to purchase ARM.
